A central goal in evolution is to explicitly connect genotype and phenotype for traits that are ecologically important. This has been an elusive goal because the genetic basis of most traits is not well understood. Coat color variation in rodents is a classic example of phenotypic variation in response to local adaptation: in many species, dorsal pelage color closely matches the soil color on which the animals live. Research on the genetics of coat color in the house mouse has produced a rich database of candidate genes and mutant effects. The combination of striking phenotypic variation in coat-color in pocket mice (Chaetodipus intermedius) and candidate pigmentation loci cloned in the laboratory mouse presents an unparalleled opportunity to investigate the genetic variation underlying a key morphological trait in nature. The proposed research will (1) document coat color variation in mice existing on both light and dark substrate, (2) screen candidate loci to identify genes contributing to observed phenotypic differences, (3) characterize mutant alleles of the implicated loci, (4) compare mutant alleles across dark populations, and (5) document selection acting on and estimate the age of the mutations. Together these studies will (1) identify the number and relative strength of genes contributing to coat color variation, (2) determine whether differences in pigmentation are due to changes in structural or regulatory regions of genes, and (3) determine if the same or different mutations occurred across dark populations.